check_rec_pres

Helper function to check whether receptor is present in target cell type

Single-cell Interpretable Tensor Decomposition (scITD) employs the
Tucker tensor decomposition to extract multicell-type gene expression patterns
that vary across donors/individuals. This tool is geared for use with single-cell
RNA-sequencing datasets consisting of many source donors. The method has a wide
range of potential applications, including the study of inter-individual variation
at the population-level, patient sub-grouping/stratification, and the analysis
of sample-level batch effects. Each "multicellular process" that is extracted
consists of (A) a multi cell type gene loadings matrix and (B) a
corresponding donor scores vector indicating the level at which the corresponding
loadings matrix is expressed in each donor. Additional methods are implemented
to aid in selecting an appropriate number of factors and to evaluate stability
of the decomposition. Additional tools are provided for downstream analysis,
including integration of gene set enrichment analysis and ligand-receptor analysis.
Tucker, L.R. (1966) <doi:10.1007/BF02289464>. Unkel, S., Hannachi, A., Trendafilov, N. T., & Jolliffe, I. T. (2011) <doi:10.1007/s13253-011-0055-9>. Zhou, G., & Cichocki, A. (2012) <doi:10.2478/v10175-012-0051-4>.

Jonathan Mitchel

scITD

Single-Cell Interpretable Tensor Decomposition

Evan Biederstedt

Peter Kharchenko

check_rec_pres function

<dl><dt>container</dt>
<dd>environment Project container that stores sub-containers
for each cell type as well as results and plots from all analyses</dd>
<dt>lig_ct_exp</dt>
<dd>numeric Scaled expression for a ligand in the source cell type</dd>
<dt>rec_elements</dt>
<dd>character One or more components of a receptor complex</dd>
<dt>target_ct</dt>
<dd>character The name of the target cell type</dd>
<dt>percentile_exp_rec</dt>
<dd>numeric The percentile of ligand expression above which
all donors need to have at least 5 cells expressing the receptor.</dd></dl>

Arguments

Helper function to check whether receptor is present in target cell type — check_rec_pres

<dl>

<dt>container</dt>
<dd>environment Project container that stores sub-containers
for each cell type as well as results and plots from all analyses</dd>


<dt>lig_ct_exp</dt>
<dd>numeric Scaled expression for a ligand in the source cell type</dd>


<dt>rec_elements</dt>
<dd>character One or more components of a receptor complex</dd>


<dt>target_ct</dt>
<dd>character The name of the target cell type</dd>


<dt>percentile_exp_rec</dt>
<dd>numeric The percentile of ligand expression above which
all donors need to have at least 5 cells expressing the receptor.</dd>

</dl>

check_rec_pres: Helper function to check whether receptor is present in target cell type

Description

Usage

Value

Arguments